MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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Rank	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

Rank	description	Value Type	Interaction Map	Filtered	red	green	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	High confidence	0	4294	15915	3.70633
	cab2. [refseq;acc:nm_033419]	Squared			0.00001	7.16592	716592
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Ranked	Low confidence	1	16	32	2
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared		0	0.00001	1.87479	187479
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Measured		1	2399.5	543.5	4.4149
		Squared			1362.75	69.9153	19.4914
		Rooted			48.9847	23.3131	2.10117
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	High confidence	0	364	0.00001	36400000
			Low confidence
		Rooted	High confidence		19.0788		1907880
			Low confidence
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked			5865	14977	2.55362
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		High confidence	1	10	24	2.4
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured			450.5	2394.5	5.31521
		Squared			48.0356	1357.07	28.2513
		Rooted			21.225	48.9336	2.30547
2	cab2. [refseq;acc:nm_033419]	Measured		0	0.00001	174	17400000
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		Low confidence	1	2399.5	543.5	4.4149
		Squared			1362.75	69.9153	19.4914
		Rooted			48.9847	23.3131	2.10117
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured		0	0.00001	89	8900000
		Rooted				9.43398	943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared				1.87479	187479
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Ranked		1	223	330	1.47982
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]		High confidence		15	28	1.86667
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		Low confidence	0	8906	21883	2.45711
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		High confidence		5865	14977	2.55362
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared			5.61325	0.00001	561325
		Rooted			12.4097		1240970
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured		1	450.5	2394.5	5.31521
		Squared			48.0356	1357.07	28.2513
		Rooted			21.225	48.9336	2.30547
3	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Ranked	Low confidence		223	330	1.47982
	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Measured			2399.5	543.5	4.4149
		Squared			1362.75	69.9153	19.4914
		Rooted			48.9847	23.3131	2.10117
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Ranked	High confidence		15	28	1.86667
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Measured			2597.5	698.5	3.71868
		Squared			1596.92	115.48	13.8285
		Rooted			50.9657	26.4292	1.92839
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	Low confidence	0	0.00001	1.87479	187479
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured				89	8900000
		Rooted				9.43398	943398
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Ranked			9607	20617	2.14604
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		High confidence		4475.84	11083.9	2.47638
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Measured			0.00001	109	10900000
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared			5.61325	0.00001	561325
		Rooted			12.4097		1240970
4	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Ranked	Low confidence	1	223	330	1.47982
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		High confidence		15	28	1.86667

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.